Background: We aimed to compare symptoms and EQ-5D-5L in acute and chronic phases between coronavirus diseases 2019 (COVID-19) patients and test-negative controls for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) during the Omicron-predominant period in Japan. Methods: Individuals aged ≥18 tested for suspected COVID-19 at a clinic in Tokyo, Japan, between January 2022 and January 2023 were invited to participate in an online survey. Participants were asked to recall and record physical and mental symptoms and EQ-5D-5L during the acute phase of illness, and at months 1, 3, and 6. We compared symptoms and EQ-5D-5L among COVID-19 patients and controls. The symptoms and EQ-5D-5L index values of male and female COVID-19 patients were also compared. Results: Overall, 302 COVID-19 patients and 77 test-negative controls were included; the median age was 42 years, and 41.2% were male. At month 3, 19.9% of the COVID-19 patients and 9.1% of the controls had symptoms. Mental symptoms and fatigue persisted for more than three months among COVID-19 patients. EQ-5D-5L mean index values of COVID-19 patients were lower than those of controls throughout the period. Female COVID-19 patients had lower EQ-5D-5L mean values than male patients over time. Conclusions: This study showed that COVID-19 patients had more symptoms at three months after testing than test-negative controls, the EQ-5D-5L mean index values of COVID-19 patients was lower than that of controls, and the decline persisted for more than six months. Female COVID-19 patients had lower EQ-5D-5L mean index values than male patients over time.